4OJ4

Crystal structure of V290M PPARgamma mutant in complex with diclofenac

PDB DOI: https://doi.org/10.2210/pdb4OJ4/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-01-20 Released: 2015-02-04
Deposition Author(s): Puhl, A.C., Webb, P., Polikarpov, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.284
R-Value Work: 0.219
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a PPAR ligand-resistance syndrome mutant

Puhl, A.C., Bernardes, A., Polikarpov, I., Webb, P.

To be published.

Macromolecule Content

Total Structure Weight: 32.14 kDa
Atom Count: 2,105
Modelled Residue Count: 260
Deposited Residue Count: 278
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	278	Homo sapiens	Mutation(s): 1 Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231 Go to UniProtKB: P37231
PHAROS: P37231 GTEx: ENSG00000132170
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37231
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DIF Query on DIF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID C₁₄ H₁₁ Cl₂ N O₂ DCOPUUMXTXDBNB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.284
R-Value Work: 0.219
R-Value Observed: 0.222
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.04	α = 90
b = 60.04	β = 90
c = 161.19	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-04

Deposition Author(s):

Puhl, A.C.

Webb, P.

Polikarpov, I.

Revision History (Full details and data files)

Version 1.0: 2015-02-04
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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4OJ4

Crystal structure of V290M PPARgamma mutant in complex with diclofenac

Crystal structure of a PPAR ligand-resistance syndrome mutant

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)